Is the sound quality that bad?
I am doing the same thing except I have the Marantz 8805 and do HDMI from a custom built pc to the 8805. Then B & W CDM7 SE fronts, 7.2 with 4 Atmos.
Is your pc or Marantz doing the rendering? If I use my 8805 the sound quality is a little better but not really worth it to me full time because I have Plex on the pc and also have all my cds ripped to flac.
And yes with optical you would lose Atmos, again I do the same thing I use my setup for movies and music. There are some things you can do for a pc like get a linear power supply to get rid of a lot of noise.
Like I said I think mine sounds pretty good for what the setup is, so until my job working on the corner starts to pay off or I hit the lotto I'm good.